name: structure-models
description: Advanced Structure Models (8 sub-skills: alloy-builder, defect-builder, heterostructure, moire-superlattice, nanowire-nanotube, quantum-dot, supercell-builder, surface-builder)
Advanced Structure Models
Overview
This skill group covers construction of advanced structural models for computational materials science. It corresponds to VASPKIT menu 08 (tasks 800--827) and provides equivalent functionality using Python tools (pymatgen, ASE, spglib), with output in CIF, POSCAR, and QE input formats.
Sub-Skills
| Sub-Skill |
Directory |
Description |
| Supercell Builder |
supercell-builder/ |
Build supercells (diagonal and non-diagonal), orthogonal supercells from non-orthogonal cells. (VASPKIT 800, 401) |
| Surface Builder |
surface-builder/ |
Build surface slabs by Miller indices using pymatgen SlabGenerator. (VASPKIT 803) |
| Alloy Builder |
alloy-builder/ |
Random substitutional alloys, SQS (Special Quasi-random Structure) generation. (VASPKIT 802) |
| Heterostructure |
heterostructure/ |
Build heterostructures from two slabs, lattice matching. (VASPKIT 804) |
| Nanowire/Nanotube |
nanowire-nanotube/ |
Build nanowires, nanotubes, quantum dots, nanoribbons. (VASPKIT 806--808) |
| Defect Builder |
defect-builder/ |
Build point defects (vacancies, substitutions, interstitials) in supercells. (VASPKIT 821--822) |
Method Decision Guide
Need a supercell?
Simple NxNxN --> supercell-builder/ (make_supercell)
Orthogonal from non-orthogonal --> supercell-builder/ (CubicSupercellTransformation)
Need a surface slab?
--> surface-builder/ (SlabGenerator by Miller index)
Need an alloy model?
Random alloy --> alloy-builder/ (random substitution)
Ordered representative --> alloy-builder/ (SQS via icet or pymatgen)
Need a heterostructure (interface)?
--> heterostructure/ (ZSLGenerator for lattice matching)
Need a nanostructure?
Nanowire --> nanowire-nanotube/ (carve from bulk)
Nanotube --> nanowire-nanotube/ (roll a sheet)
Nanoribbon --> nanowire-nanotube/ (cut from 2D sheet)
Need a defect model?
Vacancy, substitution, interstitial --> defect-builder/
Common Prerequisites
- pymatgen: pre-installed (Structure, SlabGenerator, SubstitutionTransformation, etc.)
- ASE: pre-installed (structure manipulation, visualization)
- spglib: pre-installed (symmetry analysis)
- numpy: pre-installed
- Optional:
pip install icet for SQS generation, pip install pymatgen-analysis-defects for advanced defect workflows
1---2name: structure-models3description: This skill group covers construction of advanced structural models for computational materials science. It corresponds to VASPKIT menu 08 (tasks 800--827) and provides equivalent functionality using Python tools (pymatgen, ASE, spglib), with output in CIF, POSCAR, and QE input formats.4---5
6---
7name: structure-models
8description: Advanced Structure Models (8 sub-skills: alloy-builder, defect-builder, heterostructure, moire-superlattice, nanowire-nanotube, quantum-dot, supercell-builder, surface-builder)
9---
10
11# Advanced Structure Models
12
13## Overview
14
15This skill group covers construction of advanced structural models for computational materials science. It corresponds to VASPKIT menu 08 (tasks 800--827) and provides equivalent functionality using Python tools (pymatgen, ASE, spglib), with output in CIF, POSCAR, and QE input formats.
16
17## Sub-Skills
18
19| Sub-Skill | Directory | Description |
20|---|---|---|
21| Supercell Builder | `supercell-builder/` | Build supercells (diagonal and non-diagonal), orthogonal supercells from non-orthogonal cells. (VASPKIT 800, 401) |
22| Surface Builder | `surface-builder/` | Build surface slabs by Miller indices using pymatgen SlabGenerator. (VASPKIT 803) |
23| Alloy Builder | `alloy-builder/` | Random substitutional alloys, SQS (Special Quasi-random Structure) generation. (VASPKIT 802) |
24| Heterostructure | `heterostructure/` | Build heterostructures from two slabs, lattice matching. (VASPKIT 804) |
25| Nanowire/Nanotube | `nanowire-nanotube/` | Build nanowires, nanotubes, quantum dots, nanoribbons. (VASPKIT 806--808) |
26| Defect Builder | `defect-builder/` | Build point defects (vacancies, substitutions, interstitials) in supercells. (VASPKIT 821--822) |
27
28## Method Decision Guide
29
30```
31Need a supercell?
32 Simple NxNxN --> supercell-builder/ (make_supercell)
33 Orthogonal from non-orthogonal --> supercell-builder/ (CubicSupercellTransformation)
34
35Need a surface slab?
36 --> surface-builder/ (SlabGenerator by Miller index)
37
38Need an alloy model?
39 Random alloy --> alloy-builder/ (random substitution)
40 Ordered representative --> alloy-builder/ (SQS via icet or pymatgen)
41
42Need a heterostructure (interface)?
43 --> heterostructure/ (ZSLGenerator for lattice matching)
44
45Need a nanostructure?
46 Nanowire --> nanowire-nanotube/ (carve from bulk)
47 Nanotube --> nanowire-nanotube/ (roll a sheet)
48 Nanoribbon --> nanowire-nanotube/ (cut from 2D sheet)
49
50Need a defect model?
51 Vacancy, substitution, interstitial --> defect-builder/
52```
53
54## Common Prerequisites
55
56- **pymatgen**: pre-installed (Structure, SlabGenerator, SubstitutionTransformation, etc.)
57- **ASE**: pre-installed (structure manipulation, visualization)
58- **spglib**: pre-installed (symmetry analysis)
59- **numpy**: pre-installed
60- Optional: `pip install icet` for SQS generation, `pip install pymatgen-analysis-defects` for advanced defect workflows
majiayu000